Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions

Abstract

This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.

Fig. 1

Neighbor-joining tree for binary data for preferred (1) or non-preferred/neutral (0) codons for 59 codons for 59 IBV S1 sequences and 5 G. gallus genes (B-actin β-actin, CCK cholecystokinin, vit D receptor vitamin D receptor, ovomucin alpha ovomucin α-subunit, SPFA surfactant, pulmonary-associated protein A1). Sequences with ENC (effective number of codons) values <40 and >45 are marked with asterisk and hash, respectively; sequences with ENC between 40 and 45 have no marks. Number at each nodes are bootstrap values (only >50 are shown)

Fig. 2

Expected (curve) and observed (points) effective number of codons (Y axis) and GC3 % (X axis) for 59 IBV S1 sequences (dots) and G. gallus β-actin, cholecystokinin, surfactant, pulmonary-associated protein A1, vitamin D and ovomucin genes (asterisks)